=> Building science/py-pyteomics.biolccc@py27 Started : Friday, 8 MAR 2019 at 07:22:15 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/construction/science/py-pyteomics.biolccc XDG_CONFIG_HOME=/construction/science/py-pyteomics.biolccc HOME=/construction/science/py-pyteomics.biolccc TMPDIR="/tmp" PATH=/construction/science/py-pyteomics.biolccc/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/science/py-pyteomics.biolccc XDG_CONFIG_HOME=/construction/science/py-pyteomics.biolccc HOME=/construction/science/py-pyteomics.biolccc TMPDIR="/tmp" PATH=/construction/science/py-pyteomics.biolccc/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/science/py-pyteomics.biolccc/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/pyteomics.biolccc" EXAMPLESDIR="share/examples/pyteomics.biolccc" DATADIR="share/pyteomics.biolccc" WWWDIR="www/pyteomics.biolccc" ETCDIR="etc/pyteomics.biolccc" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pyteomics.biolccc DOCSDIR=/usr/local/share/doc/pyteomics.biolccc EXAMPLESDIR=/usr/local/share/examples/pyteomics.biolccc WWWDIR=/usr/local/www/pyteomics.biolccc ETCDIR=/usr/local/etc/pyteomics.biolccc -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> NOTICE: The pyteomics.biolccc port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> py27-pyteomics.biolccc-1.5.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> py27-pyteomics.biolccc-1.5.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-pyteomics.biolccc-1.5.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: The pyteomics.biolccc port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by py27-pyteomics.biolccc-1.5.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: The pyteomics.biolccc port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by py27-pyteomics.biolccc-1.5.0 for building => SHA256 Checksum OK for pyteomics.biolccc-1.5.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: The pyteomics.biolccc port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by py27-pyteomics.biolccc-1.5.0 for building ===> Extracting for py27-pyteomics.biolccc-1.5.0 => SHA256 Checksum OK for pyteomics.biolccc-1.5.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py27-pyteomics.biolccc-1.5.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py27-pyteomics.biolccc-1.5.0 depends on package: py27-setuptools>0 - not found ===> Installing existing package /packages/All/py27-setuptools-40.8.0.txz Installing py27-setuptools-40.8.0... `-- Installing python27-2.7.15... | `-- Installing expat-2.2.6_1... | `-- Extracting expat-2.2.6_1: .......... done | `-- Installing gettext-runtime-0.19.8.1_2... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done | `-- Installing libffi-3.2.1_3... | `-- Extracting libffi-3.2.1_3: .......... done | `-- Installing libressl-2.8.3... | `-- Extracting libressl-2.8.3: .......... done | `-- Installing ncurses-6.1.20190112... | `-- Extracting ncurses-6.1.20190112: .......... done | `-- Installing readline-7.0.5... | `-- Extracting readline-7.0.5: .......... done `-- Extracting python27-2.7.15: .......... done Extracting py27-setuptools-40.8.0: .......... done Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> py27-pyteomics.biolccc-1.5.0 depends on package: py27-setuptools>0 - found ===> Returning to build of py27-pyteomics.biolccc-1.5.0 ===> py27-pyteomics.biolccc-1.5.0 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py27-pyteomics.biolccc-1.5.0 running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py27-pyteomics.biolccc-1.5.0 running build running build_py creating build creating build/lib.dragonfly-5.5-SYNTH-x86_64-2.7 creating build/lib.dragonfly-5.5-SYNTH-x86_64-2.7/pyteomics copying pyteomics/__init__.py -> build/lib.dragonfly-5.5-SYNTH-x86_64-2.7/pyteomics copying pyteomics/biolccc.py -> build/lib.dragonfly-5.5-SYNTH-x86_64-2.7/pyteomics running build_ext building 'pyteomics._biolccc' extension creating build/temp.dragonfly-5.5-SYNTH-x86_64-2.7 creating build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src creating build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core creating build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/pyteomics cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/gradientpoint.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/gradientpoint.o -DVERSION="1.5.0" In file included from src/core/gradientpoint.cpp:1: ./include/gradientpoint.h:37:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ ./include/gradientpoint.h:47:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ ./include/gradientpoint.h:51:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ src/core/gradientpoint.cpp:10:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException) ^~~~~ src/core/gradientpoint.cpp:28:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException) ^~~~~ src/core/gradientpoint.cpp:39:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException) ^~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/rod_model.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/rod_model.o -DVERSION="1.5.0" In file included from ./include/rod_model.h:5, from src/core/rod_model.cpp:8: ./include/chemicalbasis.h:109:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:113:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:128:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:176:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:217:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:238:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:330:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:337:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:344:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:351:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ In file included from src/core/rod_model.cpp:8: ./include/rod_model.h:22:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] int n1, int n2) throw(BioLCCCException); ^~~~~ ./include/rod_model.h:38:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool reversed = false) throw(BioLCCCException); ^~~~~ ./include/rod_model.h:50:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool reversed = false) throw(BioLCCCException); ^~~~~ ./include/rod_model.h:64:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ) throw(BioLCCCException); ^~~~~ In file included from src/core/rod_model.cpp:9: ./include/parsing.h:27:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const ChemicalBasis &chemBasis) throw(BioLCCCException); ^~~~~ ./include/parsing.h:44:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const double temperature) throw (BioLCCCException); ^~~~~ src/core/rod_model.cpp:20:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] int n1, int n2) throw(BioLCCCException) ^~~~~ src/core/rod_model.cpp:240:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool reversed) throw(BioLCCCException) ^~~~~ src/core/rod_model.cpp:303:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool reversed) throw(BioLCCCException) ^~~~~ src/core/rod_model.cpp:341:10: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ) throw(BioLCCCException) ^~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/biolcccexception.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/biolcccexception.o -DVERSION="1.5.0" cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/gradient.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/gradient.o -DVERSION="1.5.0" In file included from ./include/gradient.h:5, from src/core/gradient.cpp:1: ./include/gradientpoint.h:37:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ ./include/gradientpoint.h:47:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ ./include/gradientpoint.h:51:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ In file included from src/core/gradient.cpp:1: ./include/gradient.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ ./include/gradient.h:58:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ ./include/gradient.h:65:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ src/core/gradient.cpp:16:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException) ^~~~~ src/core/gradient.cpp:23:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException) ^~~~~ src/core/gradient.cpp:44:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException) ^~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/chromoconditions.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/chromoconditions.o -DVERSION="1.5.0" In file included from ./include/gradient.h:5, from ./include/chromoconditions.h:9, from src/core/chromoconditions.cpp:2: ./include/gradientpoint.h:37:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ ./include/gradientpoint.h:47:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ ./include/gradientpoint.h:51:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ In file included from ./include/chromoconditions.h:9, from src/core/chromoconditions.cpp:2: ./include/gradient.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ ./include/gradient.h:58:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ ./include/gradient.h:65:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ In file included from src/core/chromoconditions.cpp:2: ./include/chromoconditions.h:58:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:71:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:78:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:85:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:92:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:109:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:125:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:148:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:173:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:193:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:201:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:208:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ src/core/chromoconditions.cpp:22:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:48:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:65:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:83:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:99:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:122:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:160:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:186:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:209:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:236:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:260:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ src/core/chromoconditions.cpp:283:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException) ^~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/biolccc.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/biolccc.o -DVERSION="1.5.0" In file included from ./include/biolccc.h:6, from src/core/biolccc.cpp:5: ./include/chemicalbasis.h:109:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:113:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:128:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:176:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:217:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:238:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:330:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:337:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:344:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:351:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ In file included from ./include/gradient.h:5, from ./include/chromoconditions.h:9, from ./include/biolccc.h:7, from src/core/biolccc.cpp:5: ./include/gradientpoint.h:37:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ ./include/gradientpoint.h:47:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ ./include/gradientpoint.h:51:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ In file included from ./include/chromoconditions.h:9, from ./include/biolccc.h:7, from src/core/biolccc.cpp:5: ./include/gradient.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ ./include/gradient.h:58:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ ./include/gradient.h:65:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ In file included from ./include/biolccc.h:7, from src/core/biolccc.cpp:5: ./include/chromoconditions.h:58:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:71:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:78:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:85:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:92:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:109:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:125:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:148:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:173:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:193:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:201:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:208:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ In file included from ./include/biolccc.h:8, from src/core/biolccc.cpp:5: ./include/parsing.h:27:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const ChemicalBasis &chemBasis) throw(BioLCCCException); ^~~~~ ./include/parsing.h:44:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const double temperature) throw (BioLCCCException); ^~~~~ In file included from ./include/biolccc.h:9, from src/core/biolccc.cpp:5: ./include/chain_model.h:25:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const double temperature) throw (BioLCCCException); ^~~~~ In file included from ./include/biolccc.h:10, from src/core/biolccc.cpp:5: ./include/rod_model.h:22:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] int n1, int n2) throw(BioLCCCException); ^~~~~ ./include/rod_model.h:38:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool reversed = false) throw(BioLCCCException); ^~~~~ ./include/rod_model.h:50:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool reversed = false) throw(BioLCCCException); ^~~~~ ./include/rod_model.h:64:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ) throw(BioLCCCException); ^~~~~ In file included from src/core/biolccc.cpp:5: ./include/biolccc.h:47:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException); ^~~~~ ./include/biolccc.h:56:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException); ^~~~~ ./include/biolccc.h:64:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException); ^~~~~ ./include/biolccc.h:85:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException); ^~~~~ src/core/biolccc.cpp:18:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const double temperature) throw(BioLCCCException) ^~~~~ src/core/biolccc.cpp:143:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (BioLCCCException) ^~~~~ src/core/biolccc.cpp:180:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ) throw(BioLCCCException) ^~~~~ src/core/biolccc.cpp:257:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException) ^~~~~ src/core/biolccc.cpp:275:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException) ^~~~~ src/core/biolccc.cpp:287:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException) ^~~~~ src/core/biolccc.cpp:305:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException) ^~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/parsing.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/parsing.o -DVERSION="1.5.0" In file included from ./include/parsing.h:5, from src/core/parsing.cpp:2: ./include/chemicalbasis.h:109:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:113:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:128:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:176:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:217:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:238:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:330:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:337:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:344:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:351:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ In file included from src/core/parsing.cpp:2: ./include/parsing.h:27:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const ChemicalBasis &chemBasis) throw(BioLCCCException); ^~~~~ ./include/parsing.h:44:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const double temperature) throw (BioLCCCException); ^~~~~ src/core/parsing.cpp:16:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const double temperature) throw (BioLCCCException) ^~~~~ src/core/parsing.cpp:136:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const ChemicalBasis &chemBasis) throw(BioLCCCException) ^~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/chemicalbasis.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/chemicalbasis.o -DVERSION="1.5.0" In file included from src/core/chemicalbasis.cpp:1: ./include/chemicalbasis.h:109:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:113:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:128:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:176:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:217:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:238:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:330:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:337:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:344:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:351:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ src/core/chemicalbasis.cpp:43:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException) ^~~~~ src/core/chemicalbasis.cpp:55:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException) ^~~~~ src/core/chemicalbasis.cpp:82:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException) ^~~~~ src/core/chemicalbasis.cpp:99:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException) ^~~~~ src/core/chemicalbasis.cpp:115:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException) ^~~~~ src/core/chemicalbasis.cpp:142:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException) ^~~~~ src/core/chemicalbasis.cpp:215:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException) ^~~~~ src/core/chemicalbasis.cpp:231:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException) ^~~~~ src/core/chemicalbasis.cpp:248:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException) ^~~~~ src/core/chemicalbasis.cpp:265:5: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException) ^~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/chain_model.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/chain_model.o -DVERSION="1.5.0" In file included from ./include/chain_model.h:5, from src/core/chain_model.cpp:3: ./include/chemicalbasis.h:109:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:113:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:128:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:176:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:217:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:238:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:330:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:337:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:344:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:351:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ In file included from src/core/chain_model.cpp:3: ./include/chain_model.h:25:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const double temperature) throw (BioLCCCException); ^~~~~ In file included from src/core/chain_model.cpp:4: ./include/parsing.h:27:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const ChemicalBasis &chemBasis) throw(BioLCCCException); ^~~~~ ./include/parsing.h:44:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const double temperature) throw (BioLCCCException); ^~~~~ src/core/chain_model.cpp:32:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ) throw (BioLCCCException) ^~~~~ cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/chemicalgroup.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/chemicalgroup.o -DVERSION="1.5.0" cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c src/core/auxiliary.cpp -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/auxiliary.o -DVERSION="1.5.0" cc -DNDEBUG -pipe -O2 -fno-strict-aliasing -fPIC -I./include -I/usr/local/include/python2.7 -c ./pyteomics/biolccc_wrap.cxx -o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/./pyteomics/biolccc_wrap.o -DVERSION="1.5.0" In file included from ./pyteomics/biolccc_wrap.cxx:2829: ./include/chemicalbasis.h:109:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:113:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:128:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:176:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:217:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:238:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:330:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:337:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:344:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ ./include/chemicalbasis.h:351:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChemicalBasisException); ^~~~~ In file included from ./pyteomics/biolccc_wrap.cxx:2830: ./include/gradientpoint.h:37:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ ./include/gradientpoint.h:47:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ ./include/gradientpoint.h:51:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw (GradientPointException); ^~~~~ In file included from ./pyteomics/biolccc_wrap.cxx:2831: ./include/gradient.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ ./include/gradient.h:58:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ ./include/gradient.h:65:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(GradientException, GradientPointException); ^~~~~ In file included from ./pyteomics/biolccc_wrap.cxx:2832: ./include/chromoconditions.h:58:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:71:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:78:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:85:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:92:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:109:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:125:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:148:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:173:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:193:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:201:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ ./include/chromoconditions.h:208:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(ChromoConditionsException); ^~~~~ In file included from ./pyteomics/biolccc_wrap.cxx:2834: ./include/parsing.h:27:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const ChemicalBasis &chemBasis) throw(BioLCCCException); ^~~~~ ./include/parsing.h:44:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const double temperature) throw (BioLCCCException); ^~~~~ In file included from ./pyteomics/biolccc_wrap.cxx:2835: ./include/rod_model.h:22:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] int n1, int n2) throw(BioLCCCException); ^~~~~ ./include/rod_model.h:38:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool reversed = false) throw(BioLCCCException); ^~~~~ ./include/rod_model.h:50:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool reversed = false) throw(BioLCCCException); ^~~~~ ./include/rod_model.h:64:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ) throw(BioLCCCException); ^~~~~ In file included from ./pyteomics/biolccc_wrap.cxx:2836: ./include/chain_model.h:25:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const double temperature) throw (BioLCCCException); ^~~~~ In file included from ./pyteomics/biolccc_wrap.cxx:2837: ./include/biolccc.h:47:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException); ^~~~~ ./include/biolccc.h:56:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException); ^~~~~ ./include/biolccc.h:64:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException); ^~~~~ ./include/biolccc.h:85:20: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(BioLCCCException); ^~~~~ ./pyteomics/biolccc_wrap.cxx: In function 'void SWIG_Python_addvarlink(PyObject*, char*, PyObject* (*)(), int (*)(PyObject*))': ./pyteomics/biolccc_wrap.cxx:22712:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(gv->name,name,size); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ ./pyteomics/biolccc_wrap.cxx:22709:27: note: length computed here size_t size = strlen(name)+1; ~~~~~~^~~~~~ c++ -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/gradientpoint.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/rod_model.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/biolcccexception.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/gradient.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/chromoconditions.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/biolccc.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/parsing.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/chemicalbasis.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/chain_model.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/chemicalgroup.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/src/core/auxiliary.o build/temp.dragonfly-5.5-SYNTH-x86_64-2.7/./pyteomics/biolccc_wrap.o -L/usr/local/lib -lpython2.7 -o build/lib.dragonfly-5.5-SYNTH-x86_64-2.7/pyteomics/_biolccc.so -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py27-pyteomics.biolccc-1.5.0 depends on package: py27-setuptools>0 - found ===> py27-pyteomics.biolccc-1.5.0 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py27-pyteomics.biolccc-1.5.0 ===> Generating temporary packing list running install running build running build_py running build_ext running install_lib creating /construction/science/py-pyteomics.biolccc/stage/usr/local/lib/python2.7 creating /construction/science/py-pyteomics.biolccc/stage/usr/local/lib/python2.7/site-packages creating /construction/science/py-pyteomics.biolccc/stage/usr/local/lib/python2.7/site-packages/pyteomics copying build/lib.dragonfly-5.5-SYNTH-x86_64-2.7/pyteomics/_biolccc.so -> /construction/science/py-pyteomics.biolccc/stage/usr/local/lib/python2.7/site-packages/pyteomics copying build/lib.dragonfly-5.5-SYNTH-x86_64-2.7/pyteomics/biolccc.py -> /construction/science/py-pyteomics.biolccc/stage/usr/local/lib/python2.7/site-packages/pyteomics copying build/lib.dragonfly-5.5-SYNTH-x86_64-2.7/pyteomics/__init__.py -> /construction/science/py-pyteomics.biolccc/stage/usr/local/lib/python2.7/site-packages/pyteomics byte-compiling /construction/science/py-pyteomics.biolccc/stage/usr/local/lib/python2.7/site-packages/pyteomics/biolccc.py to biolccc.pyc byte-compiling /construction/science/py-pyteomics.biolccc/stage/usr/local/lib/python2.7/site-packages/pyteomics/__init__.py to __init__.pyc writing byte-compilation script '/tmp/tmpLzYeom.py' /usr/local/bin/python2.7 -O /tmp/tmpLzYeom.py removing /tmp/tmpLzYeom.py running install_egg_info running egg_info creating pyteomics.biolccc.egg-info writing pyteomics.biolccc.egg-info/PKG-INFO writing top-level names to pyteomics.biolccc.egg-info/top_level.txt writing dependency_links to pyteomics.biolccc.egg-info/dependency_links.txt writing manifest file 'pyteomics.biolccc.egg-info/SOURCES.txt' reading manifest file 'pyteomics.biolccc.egg-info/SOURCES.txt' writing manifest file 'pyteomics.biolccc.egg-info/SOURCES.txt' Copying pyteomics.biolccc.egg-info to /construction/science/py-pyteomics.biolccc/stage/usr/local/lib/python2.7/site-packages/pyteomics.biolccc-1.5.0-py2.7.egg-info running install_scripts writing list of installed files to '/construction/science/py-pyteomics.biolccc/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for py27-pyteomics.biolccc-1.5.0 file sizes/checksums [11]: . done packing files [11]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 8 MAR 2019 at 07:23:12 UTC Duration: 00:00:56